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PMID: 23701397 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

Stacks: an analysis tool set for population genomics.

Molecular ecology ·Vol. 22 ·No. 11 ·2013-06-00 ·Pages 3124-40

Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA

Abstract

Massively parallel short-read sequencing technologies, coupled with powerful software platforms, are enabling investigators to analyse tens of thousands of genetic markers. This wealth of data is rapidly expanding and allowing biological questions to be addressed with unprecedented scope and precision. The sizes of the data sets are now posing significant data processing and analysis challenges. Here we describe an extension of the Stacks software package to efficiently use genotype-by-sequencing data for studies of populations of organisms. Stacks now produces core population genomic summary statistics and SNP-by-SNP statistical tests. These statistics can be analysed across a reference genome using a smoothed sliding window. Stacks also now provides several output formats for several commonly used downstream analysis packages. The expanded population genomics functions in Stacks will make it a useful tool to harness the newest generation of massively parallel genotyping data for ecological and evolutionary genetics.

MeSH Terms
Databases, Nucleic Acid Electronic Data Processing/methods Genetic Markers Genotype High-Throughput Nucleotide Sequencing/methods Metagenomics/methods Polymorphism, Single Nucleotide Sequence Analysis, DNA Software
Chemicals
Genetic Markers
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Catchen Julian
Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA.
Hohenlohe Paul A
Bassham Susan
Amores Angel
Cresko William A
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Article Info
Journal
Molecular ecology
Abbr.
Mol Ecol
ISSN
1365-294X
DOI
10.1111/mec.12354
Published
2013-06-00
Epub
2013-00-24
Pages
3124-40
Language
English
Region
England
NLM ID
9214478
PMCID
PMC3936987
Subset
IM
Grants
NIGMS NIH HHS · P30 GM103324 · United States
NIH HHS · R24 OD011199 · United States
NIGMS NIH HHS · R24 GM079486 · United States
NCRR NIH HHS · P20RR16448 · United States
NCRR NIH HHS · R24 RR032670 · United States
NIGMS NIH HHS · 1R24GM079486-01A1 · United States
NIGMS NIH HHS · F32GM095213-01 · United States
NCRR NIH HHS · P20 RR016448 · United States
NIGMS NIH HHS · F32 GM095213 · United States
External Links
PubMed source DOI: 10.1111/mec.12354 PMC Full Text View journal details
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